When I link a note to an event in the calendar it automatically shows up itn Agendas Today section on the date of the event. This is great.
But sometimes I would like to have a note linked to an event in the calendar, but not have the note to show up in Agendas Today section on the date of the event.
Is that possible?

Not at the moment, the Today section simply shows all notes that have a calendar date associated that includes today, you cannot exclude certain notes on a day to day basis I’m afraid. One workaround/helpful thing to do would be to collapse the note you’d like to “hide”, at least it takes up less space that way.